A looming crisis caused by the failure to recruit more headteachers is reaching a flashpoint as it is revealed that up to 1,000 schools have started the new school year without a permanent head.

Teachers' leaders alarmed by the growing number of vacancies in both primary and secondary schools have told ministers in the Department for Children, Schools and Families they must act now to avert a potential disaster.

The concern comes as it emerges that the government has drawn up a secret list of heads and senior teachers, screened and approved, who will quit their jobs to help run its flagship academies when positions arise. Headteachers are furious about the move, which they say exacerbates the crisis for other schools.

'It's a tremendous own goal by the DCSF to dilute the availability of good headteachers,' said Mary Bousted, the general secretary of the Association of Teachers and Lecturers.

Mick Brookes, general secretary of the National Association of Head Teachers, has warned that almost half the leadership workforce is due to leave within the next few years. He has written to the Training and Development Agency for Schools calling for urgent action. 'Arguably the key objective for the DCSF and its agencies is the retention, supply and recruitment of headteachers,' he wrote. Brookes pointed out that applications for the post of headteacher were at an 'all-time low' in primary and special schools and revealed that between 600 and 1,000 schools were now running without permanent leadership teams.

New figures released later this month will show a sharp increase in the number of secondary schools forced to rely on temporary heads while they readvertise the posts - a problem once confined to primary schools.

Mike Stewart, headteacher of Westlands school in Torbay, Devon, and chair of the NAHT's secondary committee, said staff who would once have wanted to become heads were choosing not to because of rising levels of stress. 'Schools are now compared using 173 ranking methods - and if it is at the bottom on one of them the headteacher is sacked,' said Stewart. 'It's crackpot.' He argued that lots of schools now had to advertise two or three times for a headteacher - something that would have been 'unheard of' five or six years ago.

Governors at schools based in areas where academies are being built are particularly concerned about their staff being 'lured' away by six-figure salary offers that they cannot match.

They have reacted with anger to the news that the government has paid Veredus, a management recruitment agency, to headhunt the most successful heads and senior teachers, interview and screen them, and then place their names on a list for academies. Other schools are not allowed access to the information.

A headteacher who has been approached several times said 'astronomical' salaries of up to £130,000 were being offered to run academies smaller than the large comprehensives which pay around £75,000 to £80,000. Secrecy surrounds the list of candidates, who are not obliged to tell their governing bodies of their intentions.

Henry Stewart, chair of governors at Stoke Newington School in Hackney, east London, where a number of academies have been built, said it was not a 'level playing field'. He lost a headteacher through the Veredus system.

'My previous head told me he had been through the process and I expect most ambitious heads have,' said Stewart. 'When I rang Veredus to ask if they would circulate my headship they said, "No, it is only for academies". We would have to pay £20,000 for their services.'

Fiona Millar, the education campaigner and former aide to Cherie Blair, said: 'The department should be helping all schools to find headteachers.'

The doubling of the government's target for academies, now 400 by 2011, has resulted in a rush of adverts for principals to run them and skewed the recruitment market, said John Dunford, general secretary of the Association of School and College Leaders.

Peter Walsh, the head of Forest Hill boys' school, a performing arts college in south east London, said he has been approached by recruiters several times to run an academy, the last time by Veredus last week. 'The money they are offering - figures of £120,000 and £130,000 - is totally out of proportion when you think that it comes out of the pockets of the pupils,' he says.

The DCSF described the pool as 'a list of those who expressed an interest in becoming a principal who are informed of vacancies in academies as and when they arise'.